AMBER Archive (2006)

Subject: AMBER: PTRAJ RMS: dumping RMSd vs time data

From: r. a. (rosajaan_at_yahoo.com)
Date: Sat Nov 04 2006 - 02:58:25 CST

Dear Amber Users
   
  I heated up my system slowly from 0-375K, when I checked density, pressure,temperature, kinetic & potential , & total energy, it seemed everything is fine with the system during the simulation but when I m sending the trajectory files to ptraj I always have this error: PTRAJ RMS: dumping RMSd vs time data
  my ptraj file is:
   
  trajin heat4.crd
trajin eq4.crd
trajin md4.crd
rms first out t1eq.rms :1-388_at_CA,C,N
strip :WAT
go
   
  It would be grateful if anyone provide me with some more information about this problem. I checked the amber archive & tried to use that but it wasnt successful.
   
  Regards
   
   
   
  Amber8 Module: ptraj
  Read in control variables
Read in atom names...
Read in charges...
Read in masses...
Read in IAC (atoms involved in L-J)...
Read in NUMEX (index to excl atom list)...
Read in NNO (index for nonbond of @type)...
Read in residue labels...
 ALA SER LEU ARG ALA ASN ASP ALA PRO ILE
 VAL LEU LEU HIE GLY PHE THR GLY TRP GLY
 ARG GLU GLU MET PHE GLY PHE LYS TYR TRP
 GLY GLY VAL ARG GLY ASP ILE GLU GLN TRP
 LEU ASN ASP ASN GLY TYR ARG THR TYR THR
 LEU ALA VAL GLY PRO LEU SER SER ASN TRP
 ASP ARG ALA CYS GLU ALA TYR ALA GLN LEU
 VAL GLY GLY THR VAL ASP TYR GLY ALA ALA
 HIE ALA ALA LYS HIE GLY HIE ALA ARG PHE
 GLY ARG THR TYR PRO GLY LEU LEU PRO GLU
 LEU LYS ARG GLY GLY ARG ILE HIE ILE ILE
 ALA HIE SER GLN GLY GLY GLN THR ALA ARG
 MET LEU VAL SER LEU LEU GLU ASN GLY SER
 GLN GLU GLU ARG GLU TYR ALA LYS ALA HIE
 ASN VAL SER LEU SER PRO LEU PHE GLU GLY
 GLY HIE HIE PHE VAL LEU SER VAL THR THR
 ILE ALA THR PRO HIE ASP GLY THR THR LEU
 VAL ASN MET VAL ASP PHE THR ASP ARG PHE
 PHE ASP LEU GLN LYS ALA VAL LEU GLU ALA
 ALA ALA VAL ALA SER ASN VAL PRO TYR THR
 SER GLN VAL TYR ASP PHE LYS LEU ASP GLN
 TRP GLY LEU ARG ARG GLN PRO GLY GLU SER
 PHE ASP HIE TYR PHE GLU ARG LEU LYS ARG
 SER PRO VAL TRP THR SER THR ASP THR ALA
 ARG TYR ASP LEU SER VAL SER GLY ALA GLU
 LYS LEU ASN GLN TRP VAL GLN ALA SER PRO
 ASN THR TYR TYR LEU SER PHE SER THR GLU
 ARG THR TYR ARG GLY ALA LEU THR GLY ASN
 HIE TYR PRO GLU LEU GLY MET ASN ALA PHE
 SER ALA VAL VAL CYS ALA PRO PHE LEU GLY
 SER TYR ARG ASN PRO THR LEU GLY ILE ASP
 ASP ARG TRP LEU GLU ASN ASP GLY ILE VAL
 ASN THR VAL SER MET ASN GLY PRO LYS ARG
 GLY SER SER ASP ARG ILE VAL PRO TYR ASP
 GLY THR LEU LYS LYS GLY VAL TRP ASN ASP
 MET GLY THR TYR ASN VAL ASP HIE LEU GLU
 ILE ILE GLY VAL ASP PRO ASN PRO SER PHE
 ASP ILE ARG ALA PHE TYR LEU ARG LEU ALA
 GLU GLN LEU ALA SER LEU GLN PRO Zn C0
 Na+ Na+ WAT WAT WAT WAT WAT WAT WAT WAT
 WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
 ...
 WAT WAT WAT WAT WAT WAT WAT
Read in the residue to atom pointer list...
Read in bond parameters RK and REQ...
Read in angle parameters TK and TEQ...
Read in dihedral parameters PK, PN and PHASE...
Read in SOLTY...
Read in L-J parameters CN1 and CN2...
Read in info for bonds w/ hydrogen...
Read in info for bonds w/out hydrogen...
Read in info for angles w/ hydrogen...
Read in info for angles w/out hydrogen...
Read in info for dihedrals w/ hydrogen...
Read in info for dihedrals w/out hydrogen...
Read in excluded atom list...
Read in h-bond parameters: AG, BG, and HBCUT...
Read in atomic symbols (types)...
Read in tree information...
Read in the JOIN info...
Read in the IROTAT info...
Scanning Box
Read in box information...
Successfully completed readParm.
  Initializing state: detected PBC beta angle in prmtop that is not 90.0!
Assuming this box is a truncated octahedron, angle is 109.471221
  PTRAJ: Processing input file...
       Input is from standard input
  PTRAJ: trajin heat4.crd
Checking coordinates: heat4.crd
  PTRAJ: trajin eq4.crd
Checking coordinates: eq4.crd
  PTRAJ: trajin md4.crd
Checking coordinates: md4.crd
  PTRAJ: rms first out t1eq.rms :1-388_at_CA,C,N
Mask [:1-388_at_CA,C,N] represents 1164 atoms
  PTRAJ: strip :WAT
Mask [:WAT] represents 25755 atoms
FYI: No output trajectory specified (trajout), none will be saved.
  PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 2080 frames.
       Summary of I/O and actions follows:
  INPUT COORDINATE FILES
  File (heat4.crd) is an AMBER trajectory (with box info) with 40 sets
  File (eq4.crd) is an AMBER trajectory (with box info) with 40 sets
  File (md4.crd) is an AMBER trajectory (with box info) with 2000 sets
  OUTPUT COORDINATE FILE
  NULL entry
  ACTIONS
  1> RMS to first frame using no mass weighting
      Dumping RMSd vs. time (with time interval 1.00) to a file named t1eq.rms
      Atom selection follows :1-388_at_N,CA,C
  7> STRIP: 25755 atoms will be removed from trajectory: :393-8977
  
Processing AMBER trajectory file heat4.crd
  Set 1 ........................................
Processing AMBER trajectory file eq4.crd
  Set 1 ........................................
Processing AMBER trajectory file md4.crd
  Set 1 .................................................
Set 50 .................................................
Set 100 .................................................
Set 150 .................................................
Set 200 .................................................
Set 250 .................................................
Set 300 .................................................
Set 350 .................................................
Set 400 .................................................
Set 450 .................................................
Set 500 .................................................
Set 550 .................................................
Set 600 .................................................
Set 650 .................................................
Set 700 .................................................
Set 750 .................................................
Set 800 .................................................
Set 850 .................................................
Set 900 .................................................
Set 950 .................................................
Set 1000 .................................................
Set 1050 .................................................
Set 1100 .................................................
Set 1150 .................................................
Set 1200 .................................................
Set 1250 .................................................
Set 1300 .................................................
Set 1350 .................................................
Set 1400 .................................................
Set 1450 .................................................
Set 1500 .................................................
Set 1550 .................................................
Set 1600 .................................................
Set 1650 .................................................
Set 1700 .................................................
Set 1750 .................................................
Set 1800 .................................................
Set 1850 .................................................
Set 1900 .................................................
Set 1950 .................................................
Set 2000
  PTRAJ: Successfully read in 2080 sets and processed 2080 sets.
       Dumping accumulated results (if any)
  PTRAJ RMS: dumping RMSd vs time data

  
 
  My ptraj result:
    Dear Amber Users
   
   

   

 
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